[gmx-users] restarting a simulation

[Justin Lemkul]

On 4/7/20 11:47 AM, Daniel Burns wrote:
> You should also have an "md10.cpt" in addition to the "md10_prev.cpt"? If
> so, replace it in your command with just the md10.cpt file.  If you don't
> have it, try renaming your "_prev.cpt" file to just "md10.cpt".

The issue is not with the naming of the checkpoint file but with the 
output files specified within the checkpoint.

The simplest workaround here is simply to use -noappend and concatenate 
output later. If one moves files around, sometimes the appending 
mechanism can break for reasons that are still unclear to me.

-Justin

> Dan
>
>
> On Mon, Apr 6, 2020 at 11:06 AM Sadaf Rani <sadafrani6 at gmail.com> wrote:
>
>> Dear Gromacs users
>> I am restarting a simulation with the following command:-
>> mpirun gmx_mpi mdrun -s md10.tpr -cpi md10_prev.cpt -append
>>
>> However, I am getting following error message. All the below-named files
>> are there in my directory but it still complains the same.
>>
>> Inconsistency in user input:
>> Some output files listed in the checkpoint file md10_prev.cpt are not
>> present
>> or not named as the output files by the current program:)Expected output
>> files
>> that are present:
>>
>> Expected output files that are not present or named differently:
>> md10.log
>> md10.xtc
>> md10.trr
>> md10.edr
>> md10.xvg
>> To keep your simulation files safe, this simulation will not restart.
>> Either
>> name your
>> output files exactly the same as the previous simulation part (e.g. with
>> -deffnm), or
>> make sure all the output files are present (e.g. run from the same
>> directory
>> as the
>> previous simulation part), or instruct mdrun to write new output files with
>> mdrun -noappend.
>> In the last case, you will not be able to use appending in future for this
>> simulation.
>>
>>   I also tried without -append option.
>> Please correct me if I am wrong somewhere.
>> Thanks.
>>
>> Sadaf
>> --
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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